Locus 5654

Sequence ID	dm3.chr3L
Location	294,073 – 294,214
Length	141
Max. P	0.867674

overview

Window 5

Location	294,073 – 294,214
Length	141
Sequences	3
Columns	141
Reading direction	forward
Mean pairwise identity	92.42
Shannon entropy	0.10420
G+C content	0.37759
Mean single sequence MFE	-35.30
Consensus MFE	-30.22
Energy contribution	-30.33
Covariance contribution	0.12
Combinations/Pair	1.07
Mean z-score	-2.09
Structure conservation index	0.86
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.98
SVM RNA-class probability	0.867674
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 294073 141 + 24543557
UUGAGUAUCUAGAGUGGUGGUACGCUAAUUUCACUUACAACUAGCGGAUUCGUAUUCGCAGAAAUCAAUCGAAUCUCAGUACUCCGCAAAUAACAGCGAUUCAUCUGAUUGAAUCUACUCCUUGUCCAACUGUCUGUUUGC
..((((((..((((((((((..........)))).)))..((.((((((....))))))))............)))..)))))).(((((((((((.((((((......)))))).((.....))....)))).))))))) ( -33.70, z-score =  -1.32, R)
>droSec1.super_2 325716 140 + 7591821
UUGAGUAUCUAGAUUAGUGGUACGCUAAUUGCACUAACAACUAGCGGAUUCUGAUUC-CAGAAAUUAAUCGAAUCUCAGUACUGAGCAAAUAACAGUGAUUCAUCUUAUUGAAUCUACUAAUUGUCCAACUGUCUGUUUGC
(((((......(((((((....(((((.(((......))).)))))..(((((....-))))))))))))....)))))......((((((((((((((((((......)))))).((.....))...))))).))))))) ( -36.90, z-score =  -2.86, R)
>droSim1.chr2R 8517763 140 + 19596830
UUGAGUAUCUAGAGUAGUGGUACGCUAAUUGCACUAACAACUAGCGGAUUCGUAUUC-CAGAAAUUAUUCGAAUCUCAGUACUGAGCAAAUAACAGUGAUUCAUCUGAUUGAAUCUACUAAUUGUCCAACUGUCUAUUUGC
((((((((((.(((((.(((..(((((.(((......))).)))))...))))))))-.)))...)))))))...(((....)))((((((((((((((((((......)))))).((.....))...))))).))))))) ( -35.30, z-score =  -2.09, R)
>consensus
UUGAGUAUCUAGAGUAGUGGUACGCUAAUUGCACUAACAACUAGCGGAUUCGUAUUC_CAGAAAUUAAUCGAAUCUCAGUACUGAGCAAAUAACAGUGAUUCAUCUGAUUGAAUCUACUAAUUGUCCAACUGUCUGUUUGC
(((((......(((((((....(((((.(((......))).)))))..(((.........))))))))))....)))))......((((((((((((((((((......)))))).((.....))...))))).))))))) (-30.22 = -30.33 +   0.12)

alignment

secondary structure

dotplot

Window 6

Location	294,073 – 294,214
Length	141
Sequences	3
Columns	141
Reading direction	reverse
Mean pairwise identity	92.42
Shannon entropy	0.10420
G+C content	0.37759
Mean single sequence MFE	-36.90
Consensus MFE	-30.89
Energy contribution	-31.33
Covariance contribution	0.45
Combinations/Pair	1.02
Mean z-score	-2.15
Structure conservation index	0.84
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.90
SVM RNA-class probability	0.847942
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 294073 141 - 24543557
GCAAACAGACAGUUGGACAAGGAGUAGAUUCAAUCAGAUGAAUCGCUGUUAUUUGCGGAGUACUGAGAUUCGAUUGAUUUCUGCGAAUACGAAUCCGCUAGUUGUAAGUGAAAUUAGCGUACCACCACUCUAGAUACUCAA
(((((..((((((...((.....)).((((((......)))))))))))).))))).(((((((((((((((...(....)..))))).......((((((((........))))))))........))).)).))))).. ( -37.50, z-score =  -1.58, R)
>droSec1.super_2 325716 140 - 7591821
GCAAACAGACAGUUGGACAAUUAGUAGAUUCAAUAAGAUGAAUCACUGUUAUUUGCUCAGUACUGAGAUUCGAUUAAUUUCUG-GAAUCAGAAUCCGCUAGUUGUUAGUGCAAUUAGCGUACCACUAAUCUAGAUACUCAA
(((((..((((((...((.....)).((((((......)))))))))))).))))).......(((((((.(((((..(((((-....)))))..((((((((((....))))))))))......)))))..))).)))). ( -36.90, z-score =  -2.57, R)
>droSim1.chr2R 8517763 140 - 19596830
GCAAAUAGACAGUUGGACAAUUAGUAGAUUCAAUCAGAUGAAUCACUGUUAUUUGCUCAGUACUGAGAUUCGAAUAAUUUCUG-GAAUACGAAUCCGCUAGUUGUUAGUGCAAUUAGCGUACCACUACUCUAGAUACUCAA
((((((.((((((...((.....)).((((((......))))))))))))))))))..(((((((.((((((...........-.....))))))((((((((((....))))))))))...........))).))))... ( -36.29, z-score =  -2.31, R)
>consensus
GCAAACAGACAGUUGGACAAUUAGUAGAUUCAAUCAGAUGAAUCACUGUUAUUUGCUCAGUACUGAGAUUCGAUUAAUUUCUG_GAAUACGAAUCCGCUAGUUGUUAGUGCAAUUAGCGUACCACUACUCUAGAUACUCAA
(((((..((((((...((.....)).((((((......)))))))))))).)))))..(((((((.((((((....((((....)))).))))))((((((((((....))))))))))...........))).))))... (-30.89 = -31.33 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:52:32 2011